Directed by Mitsuo Fukuda, Gundam SEED Destiny is the sequel to Gundam SEED and the second Gundam series to be set in the Cosmic Era timeline. Gundam SEED Destiny sets the story two years after the original series and follows pilot Shinn Asuka and the rest of the crew of the ZAFT battleship Minerva's involvement in the Second Bloody Valentine War, as well as some returning characters from the previous series.Three mobile suits are stolen from ZAFT by a group called Phantom Pain, which is controlled by the Blue Cosmos terrorist organization. Shinn Asuka and the Minerva try to intervene but the group manages to escape.Shinn and the Minerva are then ordered to destroy the ruins of a space colony to prevent it from crashing into Earth. Returning character Athrun Zala decides to aid the crew of the Minerva to stop this. They find out rogue ZAFT soldiers are controlling the colony in order to cause it to crash into Earth. After failing to completely destroy the colony, a second war starts once news has spread that ZAFT soldiers cause the colony to collide on Earth.
Athrun Zala rejoins ZAFT and is assigned to the crew of the Minerva. Later in the war, Athrun becomes disaffected after PLANT Chairman Gilbert Durandal orders the destruction of his friend Kira Yamato and the Archangel and defects with Meyrin Hawke when Durandal frames him as a traitor. The leader of Blue Cosmos, Lord Djibril, orders the weapon Requiem to be fired which destroys many space colonies resulting in many deaths. The crew of the Minerva successfully kill Lord Djibril and capture the Requiem. Gilbert Durandal then announces the "Destiny Plan", a plan where a person's job or task will be based on their genetics and starts to use the Requiem to destroy anyone who opposes him. This brings Shinn and the crew of the Minerva into direct conflict with the protagonists of the first series. Kira and Athrun with their new mobile suits ZGMF-X20A Strike Freedom and ZGMF-X19A Infinite Justice respectively and their allies, defeat the ZAFT forces and destroy the Requiem. Chairman Durandal is killed by one of his own followers. Soon after, the Earth Alliance, ZAFT and the Orb union meet and decide to end the war, with Lacus Clyne acting as negotiator.